I have hypothyroidism too. Because your thyroid isn't working right, the pills they give you help make more of the hormones that it isn't producing on its own. So taking a diet pill can interfere with it. A lot of them actually say on the label to ask a physician if you have a thyroid condition.
If you take your medication every day (and eat right/exercise) then you'll notice a change. It didn't take me long.